<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2017-11-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001701108</issuerCik>
        <issuerName>Spero Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>SPRO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001030575</rptOwnerCik>
            <rptOwnerName>FORMELA JEAN FRANCOIS</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SPERO THERAPEUTICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>675 MASSACHUSETTS AVENUE, 14TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02139</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>42781</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Junior Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>245605</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F5"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F5"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>246272</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F6"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F6"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>328992</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F7"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F7"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F7"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>513318</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F7"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F7"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F7"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>602589</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F8"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The number of shares reported reflects a 1-for-6.0774 reverse stock split of the Issuer's common stock effected on October 20, 2017.</footnote>
        <footnote id="F2">Shares held by Atlas Venture Fund IX, L.P. (&quot;Atlas Venture Fund IX&quot;).  The general partner of Atlas Venture Fund IX is Atlas Venture Associates IX, L.P. (&quot;AVA IX LP&quot;). Atlas Venture Associates IX, LLC (&quot;AVA IX LLC&quot;) is the general partner of AVA IX LP. Dr. Formela is a member of AVA IX LLC and disclaims beneficial ownership of such shares, except to the extent of his pecuniary interest therein, if any.</footnote>
        <footnote id="F3">The shares of Junior preferred stock are convertible into the number of shares of common stock shown in Column 3, calculated using the conversion ratio set forth in the Issuer's Amended and Restated Certificate of Incorporation, as amended, at any time at the holder's election and automatically upon the closing of the Issuer's initial public offering. The shares have no expiration date.</footnote>
        <footnote id="F4">Share numbers give effect to the 1-for-6.0774 reverse stock split of the Issuer's common stock effected on October 20, 2017.</footnote>
        <footnote id="F5">The shares of Series A preferred stock are convertible into the number of shares of common stock shown in Column 3, calculated using the conversion ratio set forth in the Issuer's Amended and Restated Certificate of Incorporation, as amended, at any time at the holder's election and automatically upon the closing of the Issuer's initial public offering. The shares have no expiration date.</footnote>
        <footnote id="F6">The shares of Series B preferred stock are convertible into the number of shares of common stock shown in Column 3, calculated using the conversion ratio set forth in the Issuer's Amended and Restated Certificate of Incorporation, as amended, at any time at the holder's election and automatically upon the closing of the Issuer's initial public offering. The shares have no expiration date.</footnote>
        <footnote id="F7">The shares of Series C preferred stock are convertible into the number of shares of common stock shown in Column 3, calculated using the conversion ratio set forth in the Issuer's Amended and Restated Certificate of Incorporation, as amended, at any time at the holder's election and automatically upon the closing of the Issuer's initial public offering. The shares have no expiration date.</footnote>
        <footnote id="F8">Shares held by Atlas Venture Fund X, L.P. (&quot;Atlas Venture Fund X&quot;)  The general partner of Atlas Venture Fund X is Atlas Venture Associates X, L.P. (&quot;AVA X LP&quot;).   Atlas Venture Associates X, LLC (&quot;AVA X LLC&quot;) is the general partner of AVA X LP. Dr. Formela is a member of AVA X LLC and disclaims beneficial ownership of such shares, except to the extent of his pecuniary interest therein, if any.</footnote>
    </footnotes>

    <remarks>Exhibit 24.1 - Power of Attorney</remarks>

    <ownerSignature>
        <signatureName>/s/ Frank Castellucci, Attorney-in-Fact for Jean-Francois Formela</signatureName>
        <signatureDate>2017-11-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
